[gmx-users] Membrane tutorial regarding,

[RAHUL SURESH]

Yea, I haven't. I should do that first. Thank you.

On Wed, Apr 11, 2018 at 12:29 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/10/18 2:58 PM, RAHUL SURESH wrote:
>
>> Dear Justin,
>>
>> Why there are 6 equilibrations MDP's generated and how could I use one?
>> Which one should be opted for?
>>
>
> All of them, in sequence, if you want to follow the recommended Membrane
> Builder protocol (you should read that reference if you haven't already so
> you know what the Membrane Builder is doing and what the equilibration
> scheme actually does).
>
> -Justin
>
>
>
>> I found a Readme python script and is that one should be executed it?
>>
>> Thank you
>>
>> On Tue, Apr 10, 2018 at 11:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 4/10/18 2:21 PM, RAHUL SURESH wrote:
>>>
>>> Dear Users,
>>>>
>>>> Performing membrane simulations using charmm36 ff. The Protein/membrane
>>>> system is constructed using charmm-gui [POPC] . The system was then used
>>>> in
>>>> gromacs 2016.4 for simulation . Following the simulation tutorial,
>>>>
>>>> *gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter
>>>> -water spc*
>>>>
>>>> You shouldn't be doing this. CHARMM should not be used with SPC, and in
>>> fact if you built the system with CHARMM-GUI you have all the topologies
>>> and input files necessary to proceed directly with energy minimization,
>>> equilibration, etc.
>>>
>>> -Justin
>>>
>>> NH2 and COOH were chosen as terminals.
>>>
>>>> But bad luck its shows a fatal error.
>>>>
>>>> *fatal error:*
>>>> *There were 49308 missing atoms in molecule Protein if you want to use
>>>> this*
>>>> *incomplete topology anyhow, use the option -missing*
>>>>
>>>> All the missing atoms were only hydrogen.
>>>>
>>>> the water model was then changed to tip3p, even the error prevails.
>>>>
>>>> Why the ignh flag doesn't work here?
>>>> Can I go with -missing?
>>>>
>>>> Thank you
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
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>>>
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>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*